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Date & time Aug 13 '17
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In a similar vein, one might see the universe' in a single gram of fertile soil, approximately a teaspoon in size, containing all the domains (Bacteria, Archaea and Eukarya) and elements of life! The majority of life on Earth is dependent upon six critical elements: hydrogen (H), carbon (C), nitrogen (N), phosphorus (P), oxygen (O), and sulfur (S) that pass through, and are transformed by, soil organisms (the soil biota). The process of biogeochemical cycling is defined as the transformation and cycling of elements between non living (abiotic) and living (biotic) matter across land, air,imitation rolex datejust ii, and water interfaces (Madsen 2008). Biogeochemical processes are dependent upon the biota in the soil or pedosphere, the outermost layer of the Earth that is composed of soil and subject to soil formation processes. It exists at the interface of the lithosphere (rock), atmosphere (air), hydrosphere (water), and biosphere (living matter). This article addresses the role of soil biota in the pedosphere using ecological principles that link soil organisms and plants to biogeochemical processes occurring within the soil in natural and managed ecosystems.

Aggregates: Model of a Pedosphere

Soil texture (fineness or coarseness) affects plant rooting, soil structure and organic matter content. Soil texture and structure determine the pore size distribution, soil water holding capacity and the amount of water to air filled pore space in soil aggregates that provide habitat for soil organisms. Aggregates can be broadly classified into macroaggregates (>250 and microaggregates (20 250 (Six et al. 2004). An aggregate is a naturally formed assemblage of sand, silt, clay, organic matter, root hairs, microorganisms and their "glue" like secretions mucilages, extracellular polysaccharides, and hyphae (filaments) of fungi as well as the resulting pores. Soil aggregates often contain fine roots that grow into soil pores (Figure 1) associating aggregates with the rhizosphere "the zone of soil under the influence of plant roots" (Sylvia et al. 2005). Persistent binding agents like organic matter and metals stabilize microaggregates. The temporary binding agents (polysaccharides and hyphae) produced by soil organisms aid in the formation of macroaggregates contained within the more stable microaggregates. These macroaggregates function as "ecosystems or arenas of activity" (see: Arenas of Activity in the Pedosphere of a Forest) (Beare et al. 1997, Coleman et al. 2004). Thus, an aggregate is a unit of soil structure that could be considered as a very small scale model of a pedosphere. One can visualize all the interactions of gases, water, organisms and organic and inorganic constituents at the "microscale" hence the "glimpse of the universe" in a gram of soil (Figure 1). Figure 1: A soil aggregate or ped is a naturally formed assemblage of sand, silt, clay, organic matter, root hairs, microorganisms and their secretions, and resulting pores.

The Soil BiotaSoil biota consist of the micro organisms (bacteria, fungi, archaea and algae), soil animals (protozoa, nematodes, mites, springtails, spiders, insects, and earthworms) and plants (Soil Quality Institute 2001) living all or part of their lives in or on the soil or pedosphere. Millions of species of soil organisms exist but only a fraction of them have been cultured and identified. Microorganisms (fungi, archaea, bacteria, algae and cyanobacteria) are members of the soil biota but are not members of the soil fauna. The soil fauna is the collection of all the microscopic and macroscopic animals in a given soil. Soil animals can be conventionally grouped by size classes: macrofauna (cm; enchytraeids, earthworms, macroarthropods), mesofauna (mm; microarthropods, mites and collembolan), and microfauna ( protozoa, nematodes) (Figure 2). The size of a soil organism can restrict its location in the soil habitat. Smaller members of the microfauna like nematodes are basically aquatic organisms that live in the thin water films or capillary pores of aggregates preying or grazing on other aquatic microfauna such as amoebas (Figure 1). Soil protozoa are also land adapted members of aquatic microfauna that can dwell in water films in field moist soils. Water films are created by the adsorption of water to soil particles. Soil has a direct effect on the environmental conditions, habitat and nutrient sources available to the soil biota. The term pedosphere is often used interchangeably with soil and captures the concept that the soil is a habitat where the integration of spheres occurs. These spheres include the lithosphere, atmosphere, hydrosphere, and the biosphere (Brady Weil 2002) (Figure 3). Numerous biogeochemical processes regulated by soil biota occur in the pedosphere. Studies of the pedosphere range in scale from the field (km) to a soil aggregate ( to nm). Figure 2: Trophic levels in a soil food web.

2012 Nature Education Adapted from Gupta et al. 1997.

Soil organisms serve numerous roles in the pedosphere. Their most critical function is the regulation of biogeochemical transformations (Table 1). Five functions mediated by the soil biota are 1) the formation and turnover of soil organic matter (OM) that includes mineralization and sequestration of C, 2) nutrient cycling, 3) disease transmission and prevention, 4) pollutant degradation, and 5) improvement of soil structure (Gupta et al. 1997) (Figure 2). The byproducts of metabolic oxidation or reduction of C and N compounds in soils include GHG (Madsen 2008). The dominant soil GHGs consist of: carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O). Soil management practices such as N fertilization and tillage can stimulate specific microbial activities such as autotrophic nitrification, denitrification and mineralization that regulate GHG emissions (Greenhouse Gas Working Group 2010) by the oxidation and reduction of C and N.

Table 1 Examples of physiological processes catalyzed by microorganisms in biosphere habitats.

The size and composition of the microbial biomass (the combined mass of micro organisms in the soil) is dependent upon soil properties and the source(s) of C available for energy and cell synthesis. Carbon turnover, decomposition and microbial activity often lead to increases in OM and soil aggregation (see Aggregates: Model of a Pedosphere). Different ecosystems vary in their potential to support soil organisms (Table 2) and sequester C in OM. Organic C constitutes the chemical backbone of OM and is the energy source for most soil organisms. Microbial decomposition of plant residues and OM provides access to C and nutrients such as N and P required by the majority of living organisms. Mineralization of organic N to ammonium (NH4+) and additions of N fertilizers that contain NH4+ stimulate nitrification a process driven by nitrifying bacteria and archaea that transform NH4+ to nitrate (NO3 ) (Maier et al. 2009, van Elsas et al. 2007). Nitrate can then undergo an additional microbially mediated step, denitrification. Denitrifiers include bacteria and archaea (Maier et al. 2009, van Elsas et al. 2007). Both nitrification and denitrification are pathways that produce nitrous oxide (N2O).

The soil food web consists of the community of organisms that live all or part of their lives in the pedosphere and mediate the transfer of nutrients among the living (biotic) and non living (abiotic) components of the pedosphere through a series of conversions of energy and nutrients as one organism and or substance is consumed by other organisms (Sylvia et al. 2005). The mesofauna (collembolan, mites) play a role in nutrient turnover by shredding materials into smaller pieces with higher surface area providing greater access for microfauna (bacteria, fungi, mycorrhizae) that recycle the majority of C (Figure 2). All food webs contain several trophic levels or feeding positions in a food chain (Figure 2). The term grazing is used when organic C is obtained from living things. Soil organisms are part of the detrital food chain if their organic C is derived from dead materials. The detrital food chain creates new soil organic matter and cycles nutrients from existing OM. Biological systems and organisms contain fairly constant elemental ratios of carbon:nitrogen:phosphorus:sulfur (C:N:P:S). These ratios and mass balances (net change = input + output + internal change) allow scientists to determine biochemical shifts between organisms or ecosystems.

Most members of the soil fauna are chemoheterotrophs, meaning they obtain C and energy by oxidizing (metabolizing) organic compounds (Sylvia et al. 2005). Carbon sequestration limits the process of mineralization mediated by chemoheterotrophs that produce CO2. The byproducts of the mineralization process are metabolites, heat and CO2, a GHG. The production of CO2 can reduce O2 concentrations creating anoxic sites within microaggregates that result in microenvironments that differ in their content of nutrients and oxygen (van Elsas et al. 2007). These microsites are environments in which CO2 is converted to CH4+ a GHG via anaerobic respiration by archaea known as methanogens. Methane can undergo oxidation to CO2 in adjacent microsites. This process is regulated by a group of bacteria known as methanotrophs that transform CH4+ back to CO2 all in the same aggregate.

The ability of microorganisms to recycle C can provide indirect health benefits to plant communities. Soils that contain larger amounts of OM and microbial biomass tend to have higher rates of microbial activity and as such, some organisms may have the ability to out compete other organisms including plant pathogens. This type of suppression of plant pathogens is known as general suppression (Sylvia et al. 2005). Soils that contain high levels of OM may also support specific antagonistic microorganisms that have an explicit means of suppressing pathogens such as the production of antibiotics. This is an example of specific suppression. Soils that exhibit such properties are termed suppressive soils.

Microorganisms also interact directly with plants through symbiotic relationships that provide nutrients to plants while supplying C to the microorganism(s),fake oyster rolex datejust. An example of a symbiotic relationship between a soil microbe and a higher plant is the interaction of the bacterium known as a rhizobium that induces the formation of nodules on roots of soybean plants in which it fixes N for the plant using carbohydrate supplied by the plant.

Soil is a heterogeneous environment containing limited resources and multiple ecosystems ranging in size between a forest floor, the rhizosphere of a tree, an aggregate, or a single pore of an aggregate (Figure 4). These ecosystems contain areas or arenas of activity rich in detritus or plant matter representing approximately 10% of the total soil volume (Beare et al. 1995, Coleman et al. 2004). These "hot spots" of activity are widely dispersed in space and time but contain a rich biodiversity of organisms that control the biogeochemical cycling and release of nutrients transferred from one ecosystem to another by their movement (Figure 4). The link between biodiversity and biogeochemical cycling is not always evident. Other "keystone" organisms have greater influence on soil processes than their numbers would indicate. Nitrifiers are "keystone" organisms that control transformations in a portion of the N cycle but constitute less than 1% of the total microbial population.

Figure 4: Arenas of activity in soils contain hot spots.

Zones or ecosystems containing areas of activity include the (the portion of the soil volume influenced by secretions of earthworms), the porosphere (the total pore space), detritusphere (dead plant and soil biota), aggregatusphere (the sum of aggregates) and the rhizosphere.

As an example of the linkages and transport of nutrients among ecosystems in a forest consider the following scenario. Leaves fall to the forest floor. Overtime, the decaying leaf passes through the gut of a worm and is deposited in the drilosphere. Remaining leaf matter in the drilosphere located within an aggregate and additional organic materials contained within the aggregate replenish the supply of N, P, and OM used by soil organisms. These organisms decompose and mineralize detritus and OM providing a source of nutrients to plants when aggregates are part of the rhizosphere of a tree root. The mucilages that are produced by the active microorganisms feeding on detrital leaf matter and other organic materials increase the size and stability of the aggregate ecosystem. In this way, soil organisms release, transform, and relocate resources found in arenas of activity throughout the pedosphere via a number of biogeochemical cycles.

SummarySoil, or the pedosphere, is a heterogeneous environment containing limited resources widely dispersed in space and time across a continuum of ecosystems ranging in size from the microscopic to landscape scale. The interaction of soil organisms within food webs results in the release, transformation and relocation of elements throughout the pedosphere by several biogeochemical processes. Soil organisms influence soil structure by physically binding soil particles together and increasing the number and size of aggregates that provide habit for microfauna. Visualizing all the interactions of gases,imitation datejust rolex oyster perpetual, water, organisms and organic and inorganic constituents in an aggregate at the "microscale" provides us with a "glimpse of the universe" in a gram of soil.

Autotrophic nitrification: Carried out by nitrifying bacteria and archaea. It is aprocess in which ammonium is oxidized and converted to nitrite and nitrite is converted to nitrate. Inorganic N serves as the energy source. Nitrous oxide is a by product of this process. (Sylvia 2005)

Biogeochemical cycling: The transformation and cycling of elements between non living (abiotic) and living (biotic) matter across land, air, and water interfaces. (Madsen 2008)

Collembolan are microarthropods: Wingless insects a few millimeters in length and 0.2 to 2 mm in width. They are found on or near the surface of the soil and in plant litter. Populations range between 103 m 2 in agricultural soils to 106 m 2 in forest soils. (Sylvia et al,datejust rolex imitation. 2005)

Chemoheterotrophs: Organisms that obtain energy and carbon from the oxidation of organic compounds (Sylvia et al. 2005)

Denitrification: A form of anaerobic respiration that results in the conversion of NO3 to primarily N2O and elemental N (N2) (Sylvia et al. 2005)

Drilosphere: The portion of the soil volume influenced by secretions of earthworms . (Coleman et al. 2004)

Earthworms: Oligochaeta that dwell in soil. These worms have a segmented body structure. Through their activities, earthworms can stimulate microbial activity, mix soils and aide in the formation of soil structure, and translocate plant material from the surface to lower soil strata. Oligochaete is a particular class of segmented worms, including the earthworms, which have few (oligo) body bristles (chaeta). (Sylvia et al. 2005)

Enchytraeids: Small (10 20 mm in length) unpigmented terrestrial oligochaeta referred to as pot worms. (Coleman et al. 2004)

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